Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_011651165.1 RL_RS07615 aspartate aminotransferase family protein
Query= curated2:O27392 (390 letters) >NCBI__GCF_000009265.1:WP_011651165.1 Length = 455 Score = 187 bits (475), Expect = 5e-52 Identities = 137/405 (33%), Positives = 210/405 (51%), Gaps = 54/405 (13%) Query: 24 VLSHGKGATVWDIEGNSYIDCFAGVAVNSIGHAHPKVALAICHQAQRLIHSSNIYYTREQ 83 ++ G+G ++D G Y+D FAG+ +IG+ ++A A Q L + N ++ Sbjct: 35 IIQRGEGVYIFDNHGRKYLDGFAGLWCVNIGYGRREIADAATRQMNELPYY-NTFFGTTS 93 Query: 84 VELAKLLTAISPH-----DRVFFANSGAEANEGAIKLARKF---TGKSE---IIAAENSF 132 L ++ H + +FF SG+EAN+ ++AR + GKS +I+ +N + Sbjct: 94 TPATLLAQKVTSHAGERFNHIFFTGSGSEANDTWFRMARVYWSAVGKSSKKIVISRKNGY 153 Query: 133 HGRTLATVTATGQK-KYSEPFRPLPEGFKHV--PY-----GDIG-------------AMA 171 HG T+A + G K + + P+P G H+ PY GD+ A Sbjct: 154 HGSTVAGASLGGMKYMHEQGDLPIP-GIVHIGQPYWYGEGGDLSPAEFGLKVARELEAKI 212 Query: 172 DAVGDET-AAIILEPVQGEGGVIIPPEGYLKDVQELARQNDVLLILDEVQTGFGRTGAMF 230 D +G+E AA + EPVQG GVIIPPE Y +++ + + ++LL+ DEV GFGR GA F Sbjct: 213 DELGEENVAAFVAEPVQGAAGVIIPPETYWREIDRICKARNILLVTDEVICGFGRLGAWF 272 Query: 231 ASQLFGVEPDITTVAKAMGGGY-PIGAVLANERVA--MAFEPGD--HGSTFGGNPWGCAA 285 Q FGVEPD+ +AK + GY PIG VL ++RVA + E GD HG T+ G+P AA Sbjct: 273 GHQYFGVEPDLAPIAKGLSSGYLPIGGVLVSDRVADVLINEVGDFNHGFTYSGHPVCAAA 332 Query: 286 AIATIEVLMDEKLPERAA-KMGSYFLGRLRQVLHGCDAVRDIRGVGLMIGIEIDGECAGV 344 A+ + ++ +E+L ER +G YF G+ L D V + +GLM G+++ E + Sbjct: 333 ALENLRIIEEERLVERVRDDIGPYF-GKAWAALADHDLVGEAVSIGLMGGLQLAAEKSTR 391 Query: 345 VDAAR--EMGVLINCTA---GKVIRIV-------PPLVIKKEEID 377 A+ ++G L+ A G V+R PPLVI E+D Sbjct: 392 TRYAKPDQVGALVRNHALANGLVLRATGDRMLASPPLVISHAEVD 436 Lambda K H 0.320 0.138 0.404 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 484 Number of extensions: 29 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 390 Length of database: 455 Length adjustment: 32 Effective length of query: 358 Effective length of database: 423 Effective search space: 151434 Effective search space used: 151434 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory